The move means only unsweetened juice, water and low-fat milks will be sold in primary schools, with diet drinks allowed in high schools.
Drinks giants Cadbury Schweppes, Coca Cola and PepsiCo have signed up to the deal, aimed at reducing obesity which is expected to affect 87 percent of the school drinks market.
As part of his campaign to stamp out childhood obesity, Mr Clinton said that he hoped to seek similar accords with the food industry.
"We're turning a huge ship around in the middle of the ocean before it hits an iceberg," said the 42nd president, a self-described recovering junk-food addict who underwent quadruple heart bypass surgery in 2004.
The deal was brokered by the Alliance for a Healthier Generation, a joint initiative of the William J Clinton Foundation and the American Heart Association (AHA), as part of a healthy schools program.
It follows growing fears generated by reports of rising childhood obesity, for which fizzy drinks are often partly blamed because of their high calorific content and popularity with children.
Under the agreement, sugary and calorific drinks will no longer be available in vending machines and cafeterias, or at after-school activities held on school grounds.
The restrictions will also apply to drinks schools buy from the distributors for sales at sporting events and fundraisers.
The association represents major manufacturers and distributors of non-alcoholic drinks across the US.
AHA president Robert Eckel said the deal was "really the beginning of a major effort to modify childhood obesity at the level of the school systems".
The Alliance for a Healthier Generation said nearly 35 million students would be affected nationwide. The agreement applies to all public schools which have contracts with the distributors.